The exit status of the task that caused the workflow execution to fail was: 102.
The full error message was:
Error executing process > 'STAR_Fusion (34)' Caused by: Process `STAR_Fusion (34)` terminated with an error exit status (102) Command executed: set -eou pipefail STAR --genomeDir $PWD/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --runThreadN 8 --readFilesIn TARGET-20-3812482-03A-01R_RBS_withJunctionsOnGenome_dupsFlagged_r1.fq.gz TARGET-20-3812482-03A-01R_RBS_withJunctionsOnGenome_dupsFlagged_r2.fq.gz --outFileNamePrefix TARGET.20.3812482.03A.01R_ --outReadsUnmapped None --twopassMode Basic --twopass1readsN -1 --readFilesCommand "gunzip -c" --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 63004036730 --outSAMattributes NH HI NM MD AS nM jM jI XS --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --chimFilter banGenomicN /usr/local/src/STAR-Fusion/STAR-Fusion --genome_lib_dir $PWD/ctat_genome_lib_build_dir --chimeric_junction "TARGET.20.3812482.03A.01R_Chimeric.out.junction" --left_fq TARGET-20-3812482-03A-01R_RBS_withJunctionsOnGenome_dupsFlagged_r1.fq.gz --right_fq TARGET-20-3812482-03A-01R_RBS_withJunctionsOnGenome_dupsFlagged_r2.fq.gz --CPU 8 --FusionInspector inspect --examine_coding_effect --denovo_reconstruct --output_dir TARGET.20.3812482.03A.01R_ echo ---------------------------------------- echo "list all output files in /home/jlsmith3/scripts/STAR-fusion-NF" ls -1 $PWD echo ----------------------------------------- echo "list all output files in sample directory" ls -1 TARGET.20.3812482.03A.01R_ Command exit status: 102 Command output: Aug 26 02:43:11 ..... started STAR run Aug 26 02:43:11 ..... loading genome Aug 26 02:43:34 ..... started 1st pass mapping Aug 26 03:03:52 ..... finished 1st pass mapping Aug 26 03:03:53 ..... inserting junctions into the genome indices Aug 26 03:07:46 ..... started mapping Aug 26 03:46:37 ..... finished mapping Aug 26 03:46:40 ..... started sorting BAM Command error: EXITING because of fatal ERROR: not enough memory for BAM sorting: SOLUTION: re-run STAR with at least --limitBAMsortRAM 70729026558 Aug 26 03:46:40 ...... FATAL ERROR, exiting Work dir: s3://fh-pi-meshinchi-s-nextflow-scratch/a8/2cb99ebf9a49b7c3bf22359ae0ff5a Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
nextflow run -c /home/jlsmith3/nextflow.config main.nf --sample_sheet sample_sheets/TARGET_AML_Remission_JMML_APL_MDAnderson_sample_sheet.txt --star_genome_lib 's3://fh-pi-meshinchi-s-eco-public/Reference_Data/GRCh37_gencode_v19_CTAT_lib_Oct012019/ctat_genome_lib_build_dir/' --output_folder 's3://fh-pi-meshinchi-s-eco-public/TARGET_AML/RNAseq_Illumina_Data/STAR_Fusion/' --multiQC 's3://fh-pi-meshinchi-s-eco-public/TARGET_AML/RNAseq_Illumina_Data/multiQC/' --cicero_genome_lib 's3://fh-pi-meshinchi-s-eco-public/Reference_Data/CICERO_Ref/' --CICERO 's3://fh-pi-meshinchi-s-eco-public/TARGET_AML/RNAseq_Illumina_Data/CICERO/' -with-report STAR-Fusion_Remission_JMML_APL_MDAnderson_AML_report.html -cache TRUE -resume80a6aeca4093f275d7bf3365e2f9bc579d18987c-7583-4533-95dc-4969dd673b38These plots give an overview of the distribution of resource usage for each process.
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